there are many things which contradict here..
First of all no lawyer can hold anyone's passport in US. R u sure they hold your spouse passport? I doubt that.
second, officer may have found her passport in her purse there and it was presumed that she don't want to show that because of previous entry and overstay..
Consulate asking to return back very next day can be anything, , lack of time period, low staff in consulate or any other reason, you can't argue that.
Consulate was right in their decision to file a waiver, your spouse may be stayed less then 6 months but she still need waiver 212.
once alien overstays he will be deportable and inadmisable,
lets say if one of condition is not apply for her because of less time perios but second condition should apply and thats why she needs waiver.
I130 is not approved, if you didnot submit enough proof for ligimate marriage , after looking her immigration history, Immigration will raise eyebrow of marriage in entered only to precure the immigration benifits, Now burden of proof rely on you guys to prove that wrong.
there is nothing wrong what Immigration is doing in your case, Only thing , you have to submit solid proof of genuine marriage and make them revert their decision into approval of I-130.
Its a discussion, not a legal advise..